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        Note that additional data was saved in multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.24.1

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-11-25, 16:36 UTC based on data in: /gscratch/scrubbed/samwhite/gitrepos/ceasmallr/output/02.01-bismark-bowtie2-alignment-SLURM-array

        General Statistics

        Showing 48/48 rows and 2/3 columns.
        Sample Name% Aligned% Aligned
        CF01-CM01-Zygote-1-bismark
        6.0%
        CF01-CM01-Zygote_R1_001
        13.1%
        CF01-CM02-Larvae-2-bismark
        16.8%
        CF01-CM02-Larvae_R1_001
        35.0%
        CF02-CM02-Zygote-3-bismark
        8.1%
        CF02-CM02-Zygote_R1_001
        13.4%
        CF03-CM03-Zygote-4-bismark
        8.8%
        CF03-CM03-Zygote_R1_001
        20.8%
        CF03-CM04-Larvae-5-bismark
        21.6%
        CF03-CM04-Larvae_R1_001
        46.2%
        CF03-CM05-Larvae-6-bismark
        16.5%
        CF03-CM05-Larvae_R1_001
        33.9%
        CF04-CM04-Zygote_R1_001
        25.2%
        CF05-CM02-Larvae_R1_001
        35.7%
        CF05-CM05-Zygote_R1_001
        25.2%
        CF06-CM01-Zygote_R1_001
        23.4%
        CF06-CM02-Larvae_R1_001
        21.9%
        CF07-CM02-Zygote_R1_001
        11.1%
        CF08-CM03-Zygote_R1_001
        18.3%
        CF08-CM04-Larvae_R1_001
        1.0%
        CF08-CM05-Larvae_R1_001
        2.2%
        EF01-EM01-Zygote_R1_001
        22.6%
        EF02-EM02-Zygote_R1_001
        22.6%
        EF03-EM03-Zygote_R1_001
        16.1%
        EF03-EM04-Larvae_R1_001
        30.8%
        EF03-EM05-Larvae_R1_001
        28.6%
        EF04-EM04-Zygote_R1_001
        8.4%
        EF04-EM05-Larvae_R1_001
        36.2%
        EF05-EM01-Larvae-23-bismark
        14.4%
        EF05-EM01-Larvae_R1_001
        29.0%
        EF05-EM05-Zygote-24-bismark
        3.8%
        EF05-EM05-Zygote_R1_001
        6.7%
        EF05-EM06-Larvae-25-bismark
        15.7%
        EF05-EM06-Larvae_R1_001
        35.0%
        EF06-EM01-Larvae-26-bismark
        17.2%
        EF06-EM01-Larvae_R1_001
        34.2%
        EF06-EM02-Larvae-27-bismark
        16.2%
        EF06-EM02-Larvae_R1_001
        35.2%
        EF06-EM06-Larvae-28-bismark
        11.6%
        EF06-EM06-Larvae_R1_001
        25.0%
        EF07-EM01-Zygote-7-bismark
        6.0%
        EF07-EM01-Zygote_R1_001
        10.0%
        EF07-EM03-Larvae-8-bismark
        15.2%
        EF07-EM03-Larvae_R1_001
        32.9%
        EF08-EM03-Larvae-9-bismark
        17.8%
        EF08-EM03-Larvae_R1_001
        37.9%
        EF08-EM04-Larvae-10-bismark
        17.1%
        EF08-EM04-Larvae_R1_001
        34.8%

        Bismark

        Version: 0.24.2

        Maps bisulfite converted sequence reads and determine cytosine methylation states.URL: http://www.bioinformatics.babraham.ac.uk/projects/bismarkDOI: 10.1093/bioinformatics/btr167

        Alignment Rates

        Created with MultiQC

        Strand Alignment

        Created with MultiQC

        Bowtie 2 / HiSAT2

        Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4

        Paired-end alignments

        This plot shows the number of reads aligning to the reference in different ways.

        Please note that single mate alignment counts are halved to tally with pair counts properly.

        There are 6 possible types of alignment:

        • PE mapped uniquely: Pair has only one occurence in the reference genome.
        • PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
        • PE one mate mapped uniquely: One read of a pair has one occurence.
        • PE multimapped: Pair has multiple occurence.
        • PE one mate multimapped: One read of a pair has multiple occurence.
        • PE neither mate aligned: Pair has no occurence.
        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        Bismark0.24.2

        MultiQC v1.24.1 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.